This folder contains files describing the subjects in the cohort, their clinic visits and vaccinations, as well as metadata about the samples collected. 

- `participants.tsv` contains information about each participant
- `visits.tsv` contains information collected at each clinic visit
- `vaccines.tsv` contains dose dates for DTaP/Hib and PCV taken from `visits.tsv`, as well as additional health-record observations for those children for whom we had 1 year titer measurements but not complete scheduled vaccination information
- `antibiotic_usage.tsv` contains details of each recorded instance of antibiotic usage in this study. It is built by /scripts/metadata/generate_abx_usage.py from the details recorded at each clinic visit, found in `visits.tsv`
- `antibiotic_details.tsv` contains route of administration for each antibiotic in the study, by reason where necessary. This file was built manually and it used in the construction of `antibiotic_usage.tsv`
- `blood_sample_inventory.txt` contains details of the blood samples collected and used for proteomics or metabolomics analysis
- the `nasal/` subfolder contains metadata related to the nasal samples used for 16S sequencing, including tables linking sample IDs to participant and visit information, to antibiotic use and to vaccine response information. The files `nasal_titers_y1.csv`, `nasal_titers_y2.csv` and `nasal_abx_usage.csv` are generated by scripts found in `scripts/metadata`.
- the `stool/` subfolder contains metadata related to the stool samples used for metagenomic sequencing, including tables linking sample IDs to participant and visit information, to antibiotic use and to vaccine response information. The files `stool_titers_y1.csv`, `stool_titers_y2.csv` and `stool_abx_usage.csv` are generated by scripts found in `scripts/metadata`.